Merge pull request #2432 from opencb/TASK-6013 #969
GitHub Actions / Surefire tests report hdi5.1 runShortTests,runMediumTests,runLongTests
failed
Jul 6, 2024 in 0s
1811 tests run, 107 skipped, 4 failed.
Annotations
github-actions / Surefire tests report hdi5.1 runShortTests,runMediumTests,runLongTests
VariantSearchTest.testSpecialCharacter
Unknown file "a.vcf". Please, specify the study belonging. Available studies: [abyu12]
Raw output
org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException: Unknown file "a.vcf". Please, specify the study belonging. Available studies: [abyu12]
at org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException.missingStudyFor0(VariantQueryException.java:194)
at org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException.missingStudyFor(VariantQueryException.java:189)
at org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager.getResourcePair(VariantStorageMetadataManager.java:1425)
at org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager.getResourcePair(VariantStorageMetadataManager.java:1399)
at org.opencb.opencga.storage.core.metadata.VariantStorageMetadataManager.getFileIdPair(VariantStorageMetadataManager.java:763)
at org.opencb.opencga.storage.core.variant.query.VariantQueryParser.preProcessStudyParams(VariantQueryParser.java:466)
at org.opencb.opencga.storage.core.variant.query.VariantQueryParser.preProcessQuery(VariantQueryParser.java:245)
at org.opencb.opencga.storage.core.variant.query.VariantQueryParser.parseQuery(VariantQueryParser.java:177)
at org.opencb.opencga.storage.core.variant.query.VariantQueryParser.parseQuery(VariantQueryParser.java:153)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.parseQuery(VariantStorageEngine.java:1375)
at org.opencb.opencga.storage.core.variant.search.VariantSearchTest.testSpecialCharacter(VariantSearchTest.java:216)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
github-actions / Surefire tests report hdi5.1 runShortTests,runMediumTests,runLongTests
HadoopVariantStorageEngineSVTest.checkSampleIndex
Variant "1:799984<800001<800022:-:<INS>" not found!
Raw output
org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException: Variant "1:799984<800001<800022:-:<INS>" not found!
at org.opencb.opencga.storage.core.variant.adaptors.VariantQueryException.variantNotFound(VariantQueryException.java:118)
at org.opencb.opencga.storage.hadoop.variant.adaptors.sample.HBaseVariantSampleDataManager.lambda$getSampleData$5(HBaseVariantSampleDataManager.java:166)
at org.opencb.opencga.storage.hadoop.utils.HBaseManager.act(HBaseManager.java:208)
at org.opencb.opencga.storage.hadoop.variant.adaptors.sample.HBaseVariantSampleDataManager.getSampleData(HBaseVariantSampleDataManager.java:141)
at org.opencb.opencga.storage.core.variant.adaptors.sample.VariantSampleDataManager.getSampleData(VariantSampleDataManager.java:76)
at org.opencb.opencga.storage.core.variant.adaptors.sample.VariantSampleDataManager.getSampleData(VariantSampleDataManager.java:46)
at org.opencb.opencga.storage.core.variant.VariantStorageEngine.getSampleData(VariantStorageEngine.java:1240)
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngineSVTest.checkSampleIndex(HadoopVariantStorageEngineSVTest.java:77)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
github-actions / Surefire tests report hdi5.1 runShortTests,runMediumTests,runLongTests
HadoopVariantStorageEngineSplitDataTest.testLoadMultiFileDataConcurrencyFail
chr22.variant-test-file.vcf.gz
Raw output
java.lang.AssertionError: chr22.variant-test-file.vcf.gz
at org.junit.Assert.fail(Assert.java:89)
at org.junit.Assert.assertTrue(Assert.java:42)
at org.junit.Assert.assertNotNull(Assert.java:713)
at org.opencb.opencga.storage.core.variant.VariantStorageBaseTest.getResourceUri(VariantStorageBaseTest.java:173)
at org.opencb.opencga.storage.core.variant.VariantStorageBaseTest.getResourceUri(VariantStorageBaseTest.java:157)
at org.opencb.opencga.storage.core.variant.VariantStorageBaseTest.getResourceUri(VariantStorageBaseTest.java:153)
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngineSplitDataTest.testLoadMultiFileDataConcurrencyFail(HadoopVariantStorageEngineSplitDataTest.java:660)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
github-actions / Surefire tests report hdi5.1 runShortTests,runMediumTests,runLongTests
HadoopVariantStorageEngineSplitDataTest.testLoadMultiFileDataConcurrencyDeleteMany
expected:<1> but was:<2>
Raw output
java.lang.AssertionError: expected:<1> but was:<2>
at org.junit.Assert.fail(Assert.java:89)
at org.junit.Assert.failNotEquals(Assert.java:835)
at org.junit.Assert.assertEquals(Assert.java:647)
at org.junit.Assert.assertEquals(Assert.java:633)
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngineSplitDataTest.failAtLoadingFile(HadoopVariantStorageEngineSplitDataTest.java:239)
at org.opencb.opencga.storage.hadoop.variant.HadoopVariantStorageEngineSplitDataTest.testLoadMultiFileDataConcurrencyDeleteMany(HadoopVariantStorageEngineSplitDataTest.java:598)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
at org.junit.internal.runners.statements.InvokeMethod.evaluate(InvokeMethod.java:17)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:26)
at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
at org.junit.rules.TestWatcher$1.evaluate(TestWatcher.java:61)
at org.junit.rules.RunRules.evaluate(RunRules.java:20)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.junit.runners.Suite.runChild(Suite.java:128)
at org.junit.runners.Suite.runChild(Suite.java:27)
at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
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